Modern DNA sequencing machines, such as the Applied Biosystems 3730 and the Amersham MegaBACE 4000, can generate sequencing reads that exceed 1100 bases. Unfortunately, the sequencing traces typically suffer from peak blurring (broadening) and low peak to peak resolution after base 850. These later regions generally have base calls with poor quality and high numbers of errors.
To improve DNA sequencing quality, significant research effort has been expended to improve the read length of DNA sequencing traces. For example, recent advances have included the introduction of the ABI 3730 DNA sequencing instrument, the TempliPhi in vitro DNA amplification system, the BigDye sequencing chemistry, and the KB base caller. While these new tools have increased the read length obtained from automated sanger sequencing, there is still a need for better technologies and approaches.
A. Before Longtrace processing. B. Same trace after LongTrace processing.
Nucleics has over the last five years found a different means for increasing DNA sequencing read length. This approach is based on providing better processing of the trace data than that obtained from the DNA sequencers own internal software. Nucleics has developed new DNA sequencing data processing algorithms that allow 15 to 20% more useful, good quality, bases to be extracted from the raw data collected in each trace file. This improved data processing is fully compatible with sequences collected on ABI 3730, 3100, 3130 and 3730xl DNA sequencing instruments using both the 36cm & 50cm capillary array lengths. Software implementing the new trace data processing has been incorporated into a software system that allows the trace files to be automatically base called using Applied Biosystem's KB base caller. This provides a simple software based approach that avoids the need to make changes to the sequencing data collecting process while being able to be used anytime after the sequence data has been collected. This integrated software package has been called LongTrace.
The LongTrace DNA sequencing software is to be offered in two forms: 1. As a web service so that researchers can upload their sequencing trace files to a secure server for the LongTrace reprocessing, and 2. A standalone hardware/software system (LongTrace:Box) that can be used in house without the need for upload to our server.
We have put a free version of the LongTrace DNA sequencing service which can be used without registration. To try it please visit the LongTrace demo page. The high volume LongTrace FTP service can be accessed via the main LongTrace DNA sequencing service page.
You can learn more about the free standing LongTrace system by visting the LongTrace:Box overview page.
Support for the ABI 3700 sequencer has recently been added allowing 3700 users to obtain readlengths exceeding that obtained from the ABI 3730.
Last modified 28 January, 2007 | ©2006 Nucleics Pty Ltd